Variant report

Variant	rs45596833
Chromosome Location	chr18:12701326-12701327
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr18:12700925-12701767	HepG2	liver:	n/a	n/a
2	BACH1	chr18:12701325-12701369	K562	blood:	n/a	n/a
3	TCF7L2	chr18:12701301-12701485	PANC-1	pancreas:	n/a	chr18:12701426-12701442 chr18:12701398-12701414 chr18:12701398-12701414 chr18:12701426-12701442 chr18:12701430-12701439 chr18:12701401-12701410
4	GATA2	chr18:12701306-12701799	SH-SY5Y	brain:	n/a	chr18:12701444-12701453

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12677577..12680065-chr18:12699898..12703044,3	K562	blood:
2	chr18:12696763..12699239-chr18:12701108..12704411,4	MCF-7	breast:
3	chr18:12701267..12703413-chr18:12991110..12994892,3	K562	blood:
4	chr18:12700812..12705381-chr18:12946243..12950219,9	K562	blood:
5	chr18:12699667..12702594-chr18:12881299..12884281,3	K562	blood:
6	chr18:12689483..12696263-chr18:12698961..12704404,9	MCF-7	breast:
7	chr18:12701153..12703264-chr18:13056468..13058902,2	K562	blood:
8	chr18:12375314..12379217-chr18:12700733..12704866,11	K562	blood:
9	chr18:12700182..12704223-chr18:12944670..12949511,9	K562	blood:
10	chr18:12701070..12703137-chr18:12990557..12992522,2	MCF-7	breast:
11	chr18:12307184..12308743-chr18:12701040..12703824,2	K562	blood:
12	chr18:12406252..12409116-chr18:12699672..12701773,2	MCF-7	breast:
13	chr18:12657668..12659639-chr18:12701302..12703566,3	MCF-7	breast:
14	chr18:12656018..12659900-chr18:12701056..12705601,5	K562	blood:
15	chr18:12685127..12688617-chr18:12697968..12702228,5	MCF-7	breast:

No data

Variant related genes	Relation type
CEP76	TF binding region
PSMG2	TF binding region
ENSG00000176014	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000175354	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000141391	Chromatin interaction
ENSG00000101639	Chromatin interaction
ENSG00000128789	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1062235	0.92[ASN][1000 genomes]
rs1129214	0.92[ASN][1000 genomes]
rs12373207	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12373259	0.91[ASN][1000 genomes]
rs12454322	0.83[EUR][1000 genomes]
rs12455268	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12455295	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12457771	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12458097	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12458895	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12954079	0.92[ASN][1000 genomes]
rs12957555	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12957603	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12957810	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12960623	0.98[ASN][1000 genomes]
rs12960997	0.92[ASN][1000 genomes]
rs12962598	0.92[ASN][1000 genomes]
rs12963505	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12964507	0.91[ASN][1000 genomes]
rs12965733	0.87[ASN][1000 genomes]
rs12965990	0.92[ASN][1000 genomes]
rs12966246	0.86[ASN][1000 genomes]
rs12966367	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12966424	0.92[ASN][1000 genomes]
rs12968771	0.98[ASN][1000 genomes]
rs12969300	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12969446	0.92[ASN][1000 genomes]
rs12969938	0.92[ASN][1000 genomes]
rs12971256	0.87[ASN][1000 genomes]
rs1362709	0.90[ASN][1000 genomes]
rs1549011	0.92[ASN][1000 genomes]
rs1592642	0.87[ASN][1000 genomes]
rs1592643	0.87[ASN][1000 genomes]
rs17616402	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1971702	0.86[ASN][1000 genomes]
rs2011575	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2011579	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2051262	0.91[ASN][1000 genomes]
rs2302768	0.91[ASN][1000 genomes]
rs28820339	0.87[ASN][1000 genomes]
rs28832066	0.92[ASN][1000 genomes]
rs34040888	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34120824	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34277169	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34472716	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34537593	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34632667	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34690304	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34847769	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35322088	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35506854	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35634465	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35699948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35898717	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809919	0.91[ASN][1000 genomes]
rs3902981	0.85[ASN][1000 genomes]
rs4296322	0.88[ASN][1000 genomes]
rs45589535	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4633785	0.92[ASN][1000 genomes]
rs55870255	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62095975	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096023	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096046	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62096048	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6505760	0.87[ASN][1000 genomes]
rs66808227	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7233175	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7233694	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7507018	0.92[ASN][1000 genomes]
rs8083182	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8083217	0.82[ASN][1000 genomes]
rs8086099	0.87[ASN][1000 genomes]
rs8086265	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8086846	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8097134	0.87[ASN][1000 genomes]
rs9303774	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9303775	0.92[ASN][1000 genomes]
rs9303776	0.90[ASN][1000 genomes]
rs933600	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs948319	0.91[ASN][1000 genomes]
rs963920	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9945140	0.92[ASN][1000 genomes]
rs9945644	0.92[ASN][1000 genomes]
rs9945801	0.92[ASN][1000 genomes]
rs9948844	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9949293	0.92[ASN][1000 genomes]
rs9950365	0.92[ASN][1000 genomes]
rs9951576	0.92[ASN][1000 genomes]
rs9952000	0.92[ASN][1000 genomes]
rs9954112	0.92[ASN][1000 genomes]
rs9955985	0.92[ASN][1000 genomes]
rs9957880	0.91[ASN][1000 genomes]
rs9958100	0.90[ASN][1000 genomes]
rs9958412	0.92[ASN][1000 genomes]
rs9959039	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9959458	0.92[ASN][1000 genomes]
rs9959536	0.91[ASN][1000 genomes]
rs9960555	0.91[ASN][1000 genomes]
rs9961799	0.87[ASN][1000 genomes]
rs9962006	0.92[ASN][1000 genomes]
rs9963809	0.87[ASN][1000 genomes]
rs9964868	0.96[ASN][1000 genomes]
rs9966464	0.90[ASN][1000 genomes]
rs9966490	0.91[ASN][1000 genomes]
rs9966672	0.91[ASN][1000 genomes]
rs9967437	0.92[ASN][1000 genomes]
rs9967553	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
10	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
11	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs45596833	TNFSF5IP1	Cis_1M	lymphoblastoid	RTeQTL
rs45596833	RP11-861E21.2	cis	Muscle Skeletal	GTEx
rs45596833	SPIRE1	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12658800-12701800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr18:12662800-12701600	Weak transcription	Aorta	Aorta
3	chr18:12667000-12701600	Weak transcription	Gastric	stomach
4	chr18:12672200-12701400	Weak transcription	Colonic Mucosa	Colon
5	chr18:12673200-12701600	Weak transcription	Psoas Muscle	Psoas
6	chr18:12674600-12701600	Weak transcription	Right Ventricle	heart
7	chr18:12674600-12701600	Weak transcription	Small Intestine	intestine
8	chr18:12674800-12701400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr18:12678200-12701400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr18:12678400-12701600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr18:12678400-12701600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr18:12678400-12701600	Weak transcription	HSMMtube	muscle
13	chr18:12679600-12701600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr18:12680000-12701600	Weak transcription	Esophagus	oesophagus
15	chr18:12680000-12701600	Weak transcription	Ovary	ovary
16	chr18:12680800-12701400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr18:12684800-12701600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr18:12685200-12701600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:12685400-12701400	Weak transcription	Fetal Intestine Small	intestine
20	chr18:12685600-12701400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr18:12686800-12701600	Weak transcription	Lung	lung
22	chr18:12688400-12701400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:12692600-12701400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr18:12694200-12701600	Weak transcription	Fetal Stomach	stomach
25	chr18:12694600-12701600	Weak transcription	Left Ventricle	heart
26	chr18:12694600-12701600	Weak transcription	Pancreas	Pancrea
27	chr18:12694600-12701600	Weak transcription	Stomach Mucosa	stomach
28	chr18:12694800-12701400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr18:12694800-12701600	Weak transcription	Fetal Muscle Leg	muscle
30	chr18:12694800-12701600	Weak transcription	Placenta	Placenta
31	chr18:12697400-12701600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr18:12697600-12701600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr18:12697800-12701600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr18:12699200-12701400	Weak transcription	Fetal Intestine Large	intestine
35	chr18:12699200-12701400	Weak transcription	NHLF	lung
36	chr18:12699400-12701400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr18:12699600-12701600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr18:12699800-12701400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr18:12700000-12701400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr18:12700000-12701400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr18:12700000-12701600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr18:12700200-12701600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr18:12700400-12701400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr18:12700400-12701400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr18:12700400-12701400	Enhancers	Colon Smooth Muscle	Colon
46	chr18:12700600-12701400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr18:12700600-12701400	Enhancers	Liver	Liver
48	chr18:12700600-12701400	Enhancers	Brain Substantia Nigra	brain
49	chr18:12700600-12701800	Flanking Active TSS	GM12878-XiMat	blood
50	chr18:12700600-12701800	Transcr. at gene 5' and 3'	K562	blood

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